Coffee cherries were processed traditionally by the wet method that uses large quantities of water and eco-friendly methods that utilizes less water and operate mechanically to remove mucilage. The study is aimed at determining the effects of traditional and newly developed coffee processing methods on fatty acid profiles and biochemical components of two coffee cultivars. A complete randomized design was used for the study. Fresh coffee cherries for two cultivars commonly grown in Kenya, Ruiru 11 and SL 28, were processed using three different processing methods. The methods varied on the mode of mucilage removal and pulping techniques. The parchment obtained from the three processes, wet pulper, hand pulper and eco-pulper methods, were sundried and subjected to chemical analysis. Fatty acids profiles were analyzed by the use of a gas chromatography method and biochemical content; caffeine, trigonelline and chlorogenic acid were determined by HPLC analysis. The processing methods showed significant variations in the fatty acids concentrations but did not significantly affect the levels of biochemical compounds. The concentration of fatty acids ranges from 1.16 to 16.88%, with linoleic acid being dominant. The trigonelline level ranges from 1.24 to 1.36%, caffeine ranges from 1.36 to 1.45% and chlorogenic acid from 5.34 to 5.46% in the samples from the different processing methods.